c110bcc5af
* libiconv can be provided by libc, so update packages which depend on libiconv to require the iconv virtual instead * Many packages need special consideration when locating iconv depending on whether it is provided by libc (no prefix provided) or the libiconv package (in that case we want to provide a prefix) * It was also noticed that when an iconv external was provided, that there was interference with linking (this should generally be handled by Spack's compiler wrappers and bears further investigation) * Like iconv, libintl can be provided by libc or another package, namely gettext. It is not converted to a provider like libiconv because it provides additional routines. The logic is similar to that of iconv but instead of checking the provider, we check whether the gettext installation includes libintl.
210 lines
8.9 KiB
Python
210 lines
8.9 KiB
Python
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import glob
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import os
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from spack.package import *
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from spack.util.environment import EnvironmentModifications
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class Fsl(Package, CudaPackage):
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"""FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI
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brain imaging data."""
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# NOTE: A manual download is required for FSL. Spack will search your
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# current directory for the download file. Alternatively, add this file to
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# a mirror so that Spack can find it. For instructions on how to set up a
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# mirror, see https://spack.readthedocs.io/en/latest/mirrors.html
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homepage = "https://fsl.fmrib.ox.ac.uk"
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url = "file://{0}/fsl-5.0.10-sources.tar.gz".format(os.getcwd())
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manual_download = True
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version("6.0.5", sha256="df12b0b1161a26470ddf04e4c5d5d81580a04493890226207667ed8fd2b4b83f")
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version("6.0.4", sha256="58b88f38e080b05d70724d57342f58e1baf56e2bd3b98506a72b4446cad5033e")
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version("5.0.10", sha256="ca183e489320de0e502a7ba63230a7f55098917a519e8c738b005d526e700842")
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depends_on("python", type=("build", "run"))
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depends_on("expat")
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depends_on("libx11")
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depends_on("glu")
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depends_on("iconv")
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depends_on("openblas", when="@6:")
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depends_on("vtk@:8")
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conflicts("cuda_arch=none", when="+cuda", msg="must select a CUDA architecture")
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conflicts("platform=darwin", msg="currently only packaged for linux")
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patch("build_log.patch")
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patch("eddy_Makefile.patch", when="@6.0.4")
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patch("iconv.patch", when="^libiconv")
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patch("fslpython_install_v5.patch", when="@:5")
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patch("fslpython_install_v604.patch", when="@6.0.4")
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patch("fslpython_install_v605.patch", when="@6.0.5")
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# Allow fsl to use newer versions of cuda
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patch(
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"https://aur.archlinux.org/cgit/aur.git/plain/005-fix_cuda_thrust_include.patch?h=fsl",
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sha256="9471addfc2f880350eedadcb99cb8b350abf42be1c0652ccddf49e34e5e48734",
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level=2,
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)
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# allow newer compilers
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patch("libxmlpp_bool.patch")
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# These patches disable FSL's attempts to try to submit a subset of FSL
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# computations to an SGE queue system. That auto-submit mechanism only
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# works for SGE and requires someone to edit the fsl_sub script to
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# accommodate their system. These patches disable the auto submission
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# scheme and allow the fsl_sub script to behave the same on all systems,
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# and without further modification, whether the computation is submitted to
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# a "local" system, like a workstation, or as a batch job to a cluster
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# queueing system, regardless of queue system type.
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patch("fsl_sub_v5.patch", when="@:5")
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patch("fsl_sub_v6.patch", when="@6:")
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def patch(self):
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# Uncomment lines in source file to allow building from source
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with working_dir(join_path(self.stage.source_path, "etc", "fslconf")):
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sourced = FileFilter("fsl.sh")
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sourced.filter("#FSLCONFDIR", "FSLCONFDIR")
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if self.spec.satisfies("@6:"):
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sourced.filter("#FSLMACHTYPE", "FSLMACHTYPE")
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else:
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sourced.filter(r"#(FSLMACHTYPE).*", r"\1=linux_64-gcc4.8")
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if self.spec.satisfies("@:5"):
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with working_dir(join_path(self.stage.source_path, "config", "common")):
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buildproj = FileFilter("buildproj")
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buildproj.filter(r"(^FSLMACHTYPE).*", r"\1=linux_64-gcc4.8")
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# Capture the settings file
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if self.spec.satisfies("@6:"):
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settings_file = join_path(self.stage.source_path, "config", "buildSettings.mk")
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vtk_file = settings_file
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else:
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settings_file = join_path(
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self.stage.source_path, "config", "linux_64-gcc4.8", "systemvars.mk"
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)
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externals_file = join_path(
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self.stage.source_path, "config", "linux_64-gcc4.8", "externallibs.mk"
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)
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vtk_file = externals_file
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build_settings = FileFilter(settings_file)
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vtk_settings = FileFilter(vtk_file)
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build_settings.filter(r"^CUDAVER", "#CUDAVER")
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build_settings.filter(r"(^CC)\s*=.*", r"\1 = {0}".format(spack_cc))
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build_settings.filter(r"(^CXX)\s*=.*", r"\1 = {0}".format(spack_cxx))
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build_settings.filter(r"(^CXX11)\s*=.*", r"\1 = {0}".format(spack_cxx))
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vtk_suffix = self.spec["vtk"].version.up_to(2)
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vtk_lib_dir = self.spec["vtk"].prefix.lib64
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vtk_include_dir = join_path(self.spec["vtk"].prefix.include, "vtk-{0}".format(vtk_suffix))
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vtk_settings.filter(r"(^VTKDIR_INC)\s*=.*", r"\1 = {0}".format(vtk_include_dir))
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vtk_settings.filter(r"(^VTKDIR_LIB)\s*=.*", r"\1 = {0}".format(vtk_lib_dir))
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vtk_settings.filter(r"(^VTKSUFFIX)\s*=.*", r"\1 = -{0}".format(vtk_suffix))
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if "+cuda" in self.spec:
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cuda_arch = self.spec.variants["cuda_arch"].value
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cuda_gencode = " ".join(self.cuda_flags(cuda_arch))
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cuda_installation = self.spec["cuda"].prefix
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build_settings.filter(
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r"(^CUDA_INSTALLATION)\s*=.*", r"\1 = {0}".format(cuda_installation)
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)
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build_settings.filter(
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r"(^LIB_CUDA)\s*=.*", r"\1 = {0}".format(join_path(cuda_installation, "lib64"))
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)
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build_settings.filter(
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r"(^INC_CUDA)\s*=.*", r"\1 = {0}".format(join_path(cuda_installation, "include"))
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)
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build_settings.filter(
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r"(^NVCC11)\s*=.*", r"\1 = {0}".format(join_path(cuda_installation, "bin", "nvcc"))
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)
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build_settings.filter(
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r"(^NVCC)\s*=.*", r"\1 = {0}".format(join_path(cuda_installation, "bin", "nvcc"))
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)
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build_settings.filter(r"(^GENCODE_FLAGS)\s*=.*", r"\1 = {0}".format(cuda_gencode))
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if self.spec.satisfies("@6:"):
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build_settings.filter(r"(^EDDYBUILDPARAMETERS)\s*=.*", r'\1 = "cuda=1" "cpu=1"')
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build_settings.filter(r"(^fdt_MASTERBUILD)\s*=.*", r"\1 = COMPILE_GPU=1")
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build_settings.filter(r"(^ptx2_MASTERBUILD)\s*=.*", r"\1 = COMPILE_GPU=1")
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else:
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with open(settings_file, "a") as f:
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f.write("COMPILE_GPU=1\n")
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else:
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build_settings.filter(r"^CUDA_INSTALLATION", "#CUDA_INSTALLATION")
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build_settings.filter(r"^GENCODE_FLAGS", "#GENCODE_FLAGS")
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build_settings.filter(r"^LIB_CUDA", "#LIB_CUDA")
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build_settings.filter(r"^INC_CUDA", "#INC_CUDA")
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build_settings.filter(r"^NVCC", "#NVCC")
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if self.spec.satisfies("@6:"):
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build_settings.filter(r"(^EDDYBUILDPARAMETERS)\s*=.*", r'\1 = "cpu=1"')
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build_settings.filter(r"(^fdt_MASTERBUILD)\s*=.*", r"\1 = COMPILE_GPU=0")
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build_settings.filter(r"(^ptx2_MASTERBUILD)\s*=.*", r"\1 = COMPILE_GPU=0")
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filter_file(
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r'(configure_opts=".*)"',
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r'\1 --x-includes={0} --x-libraries={1}"'.format(
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self.spec["libx11"].prefix.include, self.spec["libx11"].prefix.lib
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),
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join_path("extras", "src", "tk", "unix", "fslconfigure"),
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)
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filter_file(r" -L/lib64", r"", join_path("src", "fabber_core", "Makefile"))
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def install(self, spec, prefix):
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build = Executable(join_path(self.stage.source_path, "build"))
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build()
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rm = which("rm")
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for file in glob.glob("build*"):
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rm("-f", file)
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rm("-r", "-f", "src")
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rm("-r", "-f", join_path("extras", "src"))
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rm("-r", "-f", join_path("extras", "include"))
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install_tree(".", prefix)
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@run_after("install")
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def postinstall(self):
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# The PYTHON related environment variables need to be unset here so
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# the post install script does not get confused.
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vars_to_unset = ["PYTHONPATH", "PYTHONHOME"]
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with spack.util.environment.preserve_environment(*vars_to_unset):
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for v in vars_to_unset:
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del os.environ[v]
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script = Executable(join_path(prefix, "etc", "fslconf", "post_install.sh"))
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script("-f", prefix)
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def setup_build_environment(self, env):
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if not self.stage.source_path:
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self.stage.fetch()
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self.stage.expand_archive()
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env.set("FSLDIR", self.stage.source_path)
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# Below is for sourcing purposes during building
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fslsetup = join_path(self.stage.source_path, "etc", "fslconf", "fsl.sh")
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if os.path.isfile(fslsetup):
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env.extend(EnvironmentModifications.from_sourcing_file(fslsetup))
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def setup_run_environment(self, env):
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# Set the environment variables after copying tree
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env.set("FSLDIR", self.prefix)
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fslsetup = join_path(self.prefix, "etc", "fslconf", "fsl.sh")
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if os.path.isfile(fslsetup):
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env.extend(EnvironmentModifications.from_sourcing_file(fslsetup))
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